The heparin and heparin sulfate class of glycosaminoglycans (GAG) have extraordinary variation in the secondary features of the disaccharide repeating units implicated in the modulation of some enzymes, proteins and cell membranes. We characterized oligosaccharide (oligos) from these GAG and related their structural properties to their multiple biological functions. The molecular basis of the reactions between heparin sulfates and these proteins was investigated by uv circular dichroism (CD) spectroscopy of the proteins and then complexes with oligosaccharide modulators. The two functional domains of heparin (contained within an octadecasaccharide, octadecas) that differentially activate antithrombin were investigated by low uv CD spectrocopy of their oligos along with model compounds. The disaccharide sequence between the two functional regions was elucidated, enabling us to propose a sequence for the anticoagulant octadecas. The metachromatic reaction of methylene blue with this oligos partially supports our proposed structure, which consists of alternating regions of higher and lower anionic density that are flanked by highly sulfated disaccharides. We studied the conformation of oligos using our technique of Induced CD spectroscopy. Computer-calculated theoretical extrinsic CD spectra corresponded with the experimental spectra. Oligos were isolated and characterized for experiments on neuronal development along with media conditioned over bovine embryonic kidney and human fibroblast cells. The effects of these agents on the morphological differentiation of adult chromaffin cells of the bovine adrenal (AMC), and various embryonic neuronal cells was studied. Although AMC from rat have been reported to exhibit neurite outgrowth following treatment with these agents, we found no such effect on AMC from either adult bovine or calf.